Plasma Vitamin C
Correlate Vitamin C in plasma and bone marrow
Spearman

Survival
Includes all samples, unadjusted. We also performed a landmark
analysis and analyzed this same data with peto-peto. Both were still
significant, therefore an FDR correction would not change our findings
here.
Cox model (No interaction)
Supplemntal figure XX. Forest plot for adjusted Cox
model. Cox proportional hazards regression to estimated
efficacy of vitamin C on overall survival was adjusted for patient age
at inclusion, gender, hemoglobin levels at inclusion, and whether or not
they had been diagnosed with CCUS.

Cox model (Age interaction)
Supplemental figure XX. Forest plot for adjusted Cox model in
age interaction. Cox proportional hazards regression to
estimated efficacy of vitamin C as a function of age. Age was mean
centered and converted to decades to improve hazard ratio scales.
Overall vitamin C was still effective, with evidence that it’s efficacy
decreases with age.

Cox model (TET interaction)
| TET2Mut |
32 |
31 |
| TET2neg |
22 |
24 |

Cox model (Hb1 interaction)

Cox model (Sex interaction)

Cox model (CCUS interaction)
Forest plot cannot be made due to diverging SE in treatment
## Call:
## coxph(formula = Surv(Days_FU_OS, FU_Death) ~ VitaminC + age_c +
## vitc_ccus + Male + Hb1_c + CCUS, data = df)
##
## coef exp(coef) se(coef) z p
## VitaminC -0.48013788583 0.61869807622 0.39738120115 -1.208 0.226949
## age_c 0.04289957950 1.04383306735 0.02439246075 1.759 0.078625
## vitc_ccus -18.85453900918 0.00000000648 5424.03021304527 -0.003 0.997226
## Male 0.84285200671 2.32298270049 0.46551028687 1.811 0.070203
## Hb1_c -0.67791720098 0.50767327337 0.18565236465 -3.652 0.000261
## CCUS 0.23284559292 1.26218657373 0.51029109759 0.456 0.648175
##
## Likelihood ratio test=40.98 on 6 df, p=0.0000002919
## n= 109, number of events= 35
Cox model (baseline vitamin C interaction)

2-year landmark
Maybe Figure? A 2 year landmark analysis was
performed to determine if there was still evidence of vitamin C efficacy
after removing individuals who had events prior to 2 years. This
landmark analysis ensures the effects of vitamin C had sufficient time
to reach efficacy.
Removed from landmark
| 9 |
531 |
1 |
Vitamin C |
| 12 |
403 |
1 |
Placebo |
| 17 |
113 |
1 |
Vitamin C |
| 23 |
360 |
1 |
Placebo |
| 27 |
606 |
1 |
Vitamin C |
| 30 |
621 |
1 |
Vitamin C |
| 33 |
646 |
1 |
Placebo |
| 35 |
683 |
1 |
Placebo |
| 37 |
379 |
1 |
Placebo |
| 42 |
618 |
1 |
Placebo |
| 44 |
132 |
1 |
Placebo |
| 65 |
235 |
1 |
Placebo |
| 73 |
413 |
1 |
Placebo |
| 78 |
479 |
1 |
Placebo |
| 81 |
250 |
1 |
Placebo |
| 83 |
578 |
1 |
Vitamin C |
| 87 |
391 |
1 |
Placebo |
| 95 |
701 |
0 |
Placebo |
| 96 |
666 |
0 |
Vitamin C |
| 97 |
658 |
0 |
Placebo |
| 98 |
650 |
0 |
Vitamin C |
| 99 |
650 |
0 |
Vitamin C |
| 100 |
608 |
0 |
Vitamin C |
| 101 |
594 |
0 |
Placebo |
| 102 |
539 |
0 |
Placebo |
| 103 |
152 |
1 |
Vitamin C |
| 104 |
462 |
0 |
Vitamin C |
| 105 |
401 |
0 |
Vitamin C |
| 106 |
364 |
0 |
Placebo |
| AAL2 |
509 |
1 |
Placebo |
| AAL5 |
386 |
0 |
Placebo |
| USC53 |
695 |
1 |
Placebo |
| USC59 |
714 |
0 |
Placebo |
| USC60 |
1 |
0 |
Placebo |

Per patient protocol
likelihood ratio test p-value is nearly identical to log-rank
IDs removed from main
| 1 |
| 12 |
| 17 |
| 21 |
| 23 |
| 30 |
| 32 |
| 33 |
| 35 |
| 37 |
| 43 |
| 44 |
| 48 |
| 65 |
| 72 |
| 74 |
| 76 |
| 78 |
| 81 |
| 82 |
| 87 |
| 96 |
| 103 |
| AAL2 |
| AAL4 |

LRT on treatment
| 1 |
-76.00080 |
NA |
NA |
NA |
| 0 |
-77.16977 |
-1 |
2.337937 |
0.1262567 |
Subgroups (suppl)
All subgroup analyses include only the hazard ratio with 95% CI as
these are exploratory.
TET1 or IDH1/2 at baseline
Supplemental Figure XX. Overall survival by TET2 or IDH1/2
mutation status. Hazard ratio and confidence intervals were
estimated using Cox proportional hazards models on data stratified by
TET2 and IDH1/2 mutation status. Survival curves and estimates are
consistent with the primary outcome.
LRT for interaction
| 3 |
-142.8280 |
NA |
NA |
NA |
| 2 |
-143.5895 |
-1 |
1.523109 |
0.2171495 |

Competing risk regression (progression)
For this analysis death is a competing risk of high-risk progression.
We are a bit limited in sample size and events; there are only 14
progression events. Power to detect any differences in progression is
quite low and we will have difficulty adjusting for any covariates here.
We see corroboration with our overall survival findings that death (the
dotted lines) are significantly different, however we do not have enough
evidence to determine if progression also differs.

Global Methylation
Figure XX. Global methylation changes over time by treatment
arm A) 5-mC/dG and B) 5-hmC/5-mC level for each patient at
inclusion and end-of-therapy (EOT) and the change in these measures
between inclusion and EOT. Data were analyzed using robust linear
mixed-effects models with a random intercept for each patient and an
interaction between treatment and time point to assess if measures
changed differently over time. Models also included a covariate for
batch.
Methylation IDs not in Mass Spec data
| 75 |
| 79 |
| 6 |
| 5 |
| 4 |
| 26 |
| 47 |
| 23 |
| 93 |
Delta 5-mC and 5-hmC/5-mC
TET2

baseline vitamin C

Diagnosis

Baseline 5-mC and 5-hmC/5-mC
The raw p-values should be printing in each section
Saved p-values and FDR adjustments
| mC.dG |
TET2 |
0.1991000 |
0.2844286 |
| mC.dG |
vitc_med |
0.1066000 |
0.2132000 |
| mC.dG |
vitc_ccus |
0.0078000 |
0.0390000 |
| mC.dG |
vitc_ccus |
0.6186000 |
0.6873333 |
| mC.dG |
vitc_ccus |
0.0797000 |
0.2092500 |
| hmC.mC |
TET2 |
0.0000001 |
0.0000009 |
| hmC.mC |
vitc_med |
0.5790000 |
0.6873333 |
| hmC.mC |
vitc_ccus |
0.7838000 |
0.7838000 |
| hmC.mC |
vitc_ccus |
0.1405000 |
0.2341667 |
| hmC.mC |
vitc_ccus |
0.0837000 |
0.2092500 |
TET2

baseline vitamin C

Diagnosis

5-mC/dG
All corr
##
## All
## Placebo 45
## Vitamin C 40

TET2
##
## No TET2 or IDH1/2 mutation TET2 or IDH1/2 mutation
## Placebo 16 29
## Vitamin C 18 22

LOF TET2
##
## TET2 WT signature TET2 hypermethylation signature
## Placebo 25 15
## Vitamin C 21 14

Vitamin C Severe
##
## Severe (< 11.4 μmol/L) All others
## Placebo 4 41
## Vitamin C 2 38

Diagnosis (CCUS)
##
## CCUS MDS MDS/MPN
## Placebo 16 17 11
## Vitamin C 15 17 7

5-hmC/dG
All corr
##
## All
## Placebo 45
## Vitamin C 40

TET2
##
## No TET2 or IDH1/2 mutation TET2 or IDH1/2 mutation
## Placebo 16 29
## Vitamin C 18 22

LOF TET2
##
## TET2 WT signature TET2 hypermethylation signature
## Placebo 25 15
## Vitamin C 21 14

Vitamin C Severe
##
## Severe (< 11.4 μmol/L) All others
## Placebo 4 41
## Vitamin C 2 38

Diagnosis (CCUS)
##
## CCUS MDS MDS/MPN
## Placebo 16 17 11
## Vitamin C 15 17 7

5-hmC/5-mC
All corr
##
## All
## Placebo 45
## Vitamin C 40

TET2
##
## No TET2 or IDH1/2 mutation TET2 or IDH1/2 mutation
## Placebo 16 29
## Vitamin C 18 22

LOF TET2
##
## TET2 WT signature TET2 hypermethylation signature
## Placebo 25 15
## Vitamin C 21 14

Vitamin C Severe
##
## Severe (< 11.4 μmol/L) All others
## Placebo 4 41
## Vitamin C 2 38

Diagnosis (CCUS)
##
## CCUS MDS MDS/MPN
## Placebo 16 17 11
## Vitamin C 15 17 7
